[{"page":"12949-12954","abstract":[{"lang":"eng","text":"DNA has become a prime material for assembling complex three-dimensional objects that promise utility in various areas of application. However, achieving user-defined goals with DNA objects has been hampered by the difficulty to prepare them at arbitrary concentrations and in user-defined solution conditions. Here, we describe a method that solves this problem. The method is based on poly(ethylene glycol)-induced depletion of species with high molecular weight. We demonstrate that our method is applicable to a wide spectrum of DNA shapes and that it achieves excellent recovery yields of target objects up to 97 %, while providing efficient separation from non-integrated DNA strands. DNA objects may be prepared at concentrations up to the limit of solubility, including the possibility for bringing DNA objects into a solid phase. Due to the fidelity and simplicity of our method we anticipate that it will help to catalyze the development of new types of applications that use self-assembled DNA objects."}],"date_updated":"2023-11-07T12:14:30Z","oa_version":"Published Version","month":"11","type":"journal_article","volume":126,"date_created":"2023-09-06T12:51:14Z","year":"2014","_id":"14301","publication_status":"published","oa":1,"date_published":"2014-11-17T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/ange.201405991"}],"status":"public","external_id":{"pmid":["25346175"]},"extern":"1","intvolume":"       126","citation":{"mla":"Stahl, Evi, et al. “Facile and Scalable Preparation of Pure and Dense DNA Origami Solutions.” <i>Angewandte Chemie International Edition</i>, vol. 126, no. 47, Wiley, 2014, pp. 12949–54, doi:<a href=\"https://doi.org/10.1002/ange.201405991\">10.1002/ange.201405991</a>.","ista":"Stahl E, Martin T, Praetorius FM, Dietz H. 2014. Facile and scalable preparation of pure and dense DNA origami solutions. Angewandte Chemie International Edition. 126(47), 12949–12954.","apa":"Stahl, E., Martin, T., Praetorius, F. M., &#38; Dietz, H. (2014). Facile and scalable preparation of pure and dense DNA origami solutions. <i>Angewandte Chemie International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/ange.201405991\">https://doi.org/10.1002/ange.201405991</a>","ama":"Stahl E, Martin T, Praetorius FM, Dietz H. Facile and scalable preparation of pure and dense DNA origami solutions. <i>Angewandte Chemie International Edition</i>. 2014;126(47):12949-12954. doi:<a href=\"https://doi.org/10.1002/ange.201405991\">10.1002/ange.201405991</a>","short":"E. Stahl, T. Martin, F.M. Praetorius, H. Dietz, Angewandte Chemie International Edition 126 (2014) 12949–12954.","ieee":"E. Stahl, T. Martin, F. M. Praetorius, and H. Dietz, “Facile and scalable preparation of pure and dense DNA origami solutions,” <i>Angewandte Chemie International Edition</i>, vol. 126, no. 47. Wiley, pp. 12949–12954, 2014.","chicago":"Stahl, Evi, Thomas Martin, Florian M Praetorius, and Hendrik Dietz. “Facile and Scalable Preparation of Pure and Dense DNA Origami Solutions.” <i>Angewandte Chemie International Edition</i>. Wiley, 2014. <a href=\"https://doi.org/10.1002/ange.201405991\">https://doi.org/10.1002/ange.201405991</a>."},"author":[{"full_name":"Stahl, Evi","last_name":"Stahl","first_name":"Evi"},{"full_name":"Martin, Thomas","last_name":"Martin","first_name":"Thomas"},{"last_name":"Praetorius","first_name":"Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","full_name":"Praetorius, Florian M"},{"first_name":"Hendrik","last_name":"Dietz","full_name":"Dietz, Hendrik"}],"day":"17","title":"Facile and scalable preparation of pure and dense DNA origami solutions","publisher":"Wiley","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"publication":"Angewandte Chemie International Edition","scopus_import":"1","article_processing_charge":"No","article_type":"original","publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"doi":"10.1002/ange.201405991","quality_controlled":"1","language":[{"iso":"eng"}],"issue":"47"},{"_id":"9050","year":"2014","volume":10,"date_created":"2021-02-01T13:43:31Z","oa_version":"Preprint","type":"journal_article","month":"03","abstract":[{"text":"Self-propelled particles can exhibit surprising non-equilibrium behaviors, and how they interact with obstacles or boundaries remains an important open problem. Here we show that chemically propelled micro-rods can be captured, with little change in their speed, into close orbits around solid spheres resting on or near a horizontal plane. We show that this interaction between sphere and particle is short-range, occurring even for spheres smaller than the particle length, and for a variety of sphere materials. We consider a simple model, based on lubrication theory, of a force- and torque-free swimmer driven by a surface slip (the phoretic propulsion mechanism) and moving near a solid surface. The model demonstrates capture, or movement towards the surface, and yields speeds independent of distance. This study reveals the crucial aspects of activity–driven interactions of self-propelled particles with passive objects, and brings into question the use of colloidal tracers as probes of active matter.","lang":"eng"}],"date_updated":"2023-02-23T13:47:35Z","extern":"1","intvolume":"        10","citation":{"short":"D. Takagi, J.A. Palacci, A.B. Braunschweig, M.J. Shelley, J. Zhang, Soft Matter 10 (2014).","chicago":"Takagi, Daisuke, Jérémie A Palacci, Adam B. Braunschweig, Michael J. Shelley, and Jun Zhang. “Hydrodynamic Capture of Microswimmers into Sphere-Bound Orbits.” <i>Soft Matter</i>. Royal Society of Chemistry , 2014. <a href=\"https://doi.org/10.1039/c3sm52815d\">https://doi.org/10.1039/c3sm52815d</a>.","ieee":"D. Takagi, J. A. Palacci, A. B. Braunschweig, M. J. Shelley, and J. Zhang, “Hydrodynamic capture of microswimmers into sphere-bound orbits,” <i>Soft Matter</i>, vol. 10, no. 11. Royal Society of Chemistry , 2014.","apa":"Takagi, D., Palacci, J. A., Braunschweig, A. B., Shelley, M. J., &#38; Zhang, J. (2014). Hydrodynamic capture of microswimmers into sphere-bound orbits. <i>Soft Matter</i>. Royal Society of Chemistry . <a href=\"https://doi.org/10.1039/c3sm52815d\">https://doi.org/10.1039/c3sm52815d</a>","ista":"Takagi D, Palacci JA, Braunschweig AB, Shelley MJ, Zhang J. 2014. Hydrodynamic capture of microswimmers into sphere-bound orbits. Soft Matter. 10(11), 1784.","mla":"Takagi, Daisuke, et al. “Hydrodynamic Capture of Microswimmers into Sphere-Bound Orbits.” <i>Soft Matter</i>, vol. 10, no. 11, 1784, Royal Society of Chemistry , 2014, doi:<a href=\"https://doi.org/10.1039/c3sm52815d\">10.1039/c3sm52815d</a>.","ama":"Takagi D, Palacci JA, Braunschweig AB, Shelley MJ, Zhang J. Hydrodynamic capture of microswimmers into sphere-bound orbits. <i>Soft Matter</i>. 2014;10(11). doi:<a href=\"https://doi.org/10.1039/c3sm52815d\">10.1039/c3sm52815d</a>"},"status":"public","external_id":{"arxiv":["1309.5662"],"pmid":["24800268"]},"date_published":"2014-03-21T00:00:00Z","main_file_link":[{"url":"https://arxiv.org/abs/1309.5662","open_access":"1"}],"publication_status":"published","oa":1,"publication":"Soft Matter","article_type":"original","scopus_import":"1","article_processing_charge":"No","publisher":"Royal Society of Chemistry ","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","pmid":1,"article_number":"1784","arxiv":1,"title":"Hydrodynamic capture of microswimmers into sphere-bound orbits","author":[{"first_name":"Daisuke","last_name":"Takagi","full_name":"Takagi, Daisuke"},{"last_name":"Palacci","first_name":"Jérémie A","orcid":"0000-0002-7253-9465","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","full_name":"Palacci, Jérémie A"},{"last_name":"Braunschweig","first_name":"Adam B.","full_name":"Braunschweig, Adam B."},{"full_name":"Shelley, Michael J.","first_name":"Michael J.","last_name":"Shelley"},{"full_name":"Zhang, Jun","first_name":"Jun","last_name":"Zhang"}],"day":"21","keyword":["General Chemistry","Condensed Matter Physics"],"issue":"11","language":[{"iso":"eng"}],"doi":"10.1039/c3sm52815d","quality_controlled":"1","publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]}},{"oa":1,"publication_status":"published","date_published":"2014-11-28T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1098/rsta.2013.0372"}],"external_id":{"arxiv":["1410.7278"],"pmid":["25332383"]},"status":"public","extern":"1","intvolume":"       372","citation":{"apa":"Palacci, J. A., Sacanna, S., Kim, S.-H., Yi, G.-R., Pine, D. J., &#38; Chaikin, P. M. (2014). Light-activated self-propelled colloids. <i>Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rsta.2013.0372\">https://doi.org/10.1098/rsta.2013.0372</a>","ista":"Palacci JA, Sacanna S, Kim S-H, Yi G-R, Pine DJ, Chaikin PM. 2014. Light-activated self-propelled colloids. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. 372(2029), 20130372.","mla":"Palacci, Jérémie A., et al. “Light-Activated Self-Propelled Colloids.” <i>Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>, vol. 372, no. 2029, 20130372, The Royal Society, 2014, doi:<a href=\"https://doi.org/10.1098/rsta.2013.0372\">10.1098/rsta.2013.0372</a>.","ama":"Palacci JA, Sacanna S, Kim S-H, Yi G-R, Pine DJ, Chaikin PM. Light-activated self-propelled colloids. <i>Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>. 2014;372(2029). doi:<a href=\"https://doi.org/10.1098/rsta.2013.0372\">10.1098/rsta.2013.0372</a>","short":"J.A. Palacci, S. Sacanna, S.-H. Kim, G.-R. Yi, D.J. Pine, P.M. Chaikin, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 372 (2014).","chicago":"Palacci, Jérémie A, S. Sacanna, S.-H. Kim, G.-R. Yi, D. J. Pine, and P. M. Chaikin. “Light-Activated Self-Propelled Colloids.” <i>Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>. The Royal Society, 2014. <a href=\"https://doi.org/10.1098/rsta.2013.0372\">https://doi.org/10.1098/rsta.2013.0372</a>.","ieee":"J. A. Palacci, S. Sacanna, S.-H. Kim, G.-R. Yi, D. J. Pine, and P. M. Chaikin, “Light-activated self-propelled colloids,” <i>Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>, vol. 372, no. 2029. The Royal Society, 2014."},"oa_version":"Published Version","month":"11","type":"journal_article","date_updated":"2021-02-22T10:44:16Z","abstract":[{"lang":"eng","text":"Light-activated self-propelled colloids are synthesized and their active motion is studied using optical microscopy. We propose a versatile route using different photoactive materials, and demonstrate a multiwavelength activation and propulsion. Thanks to the photoelectrochemical properties of two semiconductor materials (α-Fe2O3 and TiO2), a light with an energy higher than the bandgap triggers the reaction of decomposition of hydrogen peroxide and produces a chemical cloud around the particle. It induces a phoretic attraction with neighbouring colloids as well as an osmotic self-propulsion of the particle on the substrate. We use these mechanisms to form colloidal cargos as well as self-propelled particles where the light-activated component is embedded into a dielectric sphere. The particles are self-propelled along a direction otherwise randomized by thermal fluctuations, and exhibit a persistent random walk. For sufficient surface density, the particles spontaneously form ‘living crystals’ which are mobile, break apart and reform. Steering the particle with an external magnetic field, we show that the formation of the dense phase results from the collisions heads-on of the particles. This effect is intrinsically non-equilibrium and a novel principle of organization for systems without detailed balance. Engineering families of particles self-propelled by different wavelength demonstrate a good understanding of both the physics and the chemistry behind the system and points to a general route for designing new families of self-propelled particles."}],"volume":372,"date_created":"2021-02-18T14:31:11Z","year":"2014","_id":"9166","publication_identifier":{"eissn":["1471-2962"],"issn":["1364-503X"]},"doi":"10.1098/rsta.2013.0372","quality_controlled":"1","keyword":["General Engineering","General Physics and Astronomy","General Mathematics"],"issue":"2029","language":[{"iso":"eng"}],"author":[{"last_name":"Palacci","first_name":"Jérémie A","full_name":"Palacci, Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","orcid":"0000-0002-7253-9465"},{"first_name":"S.","last_name":"Sacanna","full_name":"Sacanna, S."},{"last_name":"Kim","first_name":"S.-H.","full_name":"Kim, S.-H."},{"first_name":"G.-R.","last_name":"Yi","full_name":"Yi, G.-R."},{"last_name":"Pine","first_name":"D. J.","full_name":"Pine, D. J."},{"first_name":"P. M.","last_name":"Chaikin","full_name":"Chaikin, P. M."}],"day":"28","article_number":"20130372","arxiv":1,"title":"Light-activated self-propelled colloids","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","publisher":"The Royal Society","pmid":1,"publication":"Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences","article_type":"original","scopus_import":"1","article_processing_charge":"No"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Cell Press","acknowledgement":"We thank F. Gao, R.E. Ward, S. Luschnig, T. Okajima, M. Affolter, D. Bilder, E. Knust, T. Tanaka, A. Nakamura, C. Samakovlis, K. Saigo, M. Furuse, the Bloomington Stock Center, Drosophila Genetic Resource Center in Kyoto, Japan, and the Developmental Studies Hybridoma Bank for generously providing antibodies and fly stocks; H. Wada for UAS-3×TagRFP fly and dye injection; Y.H. Zhang for plasmid and protocol for CBP preparation; and J. Prost and J.F. Joanny for their support for the project and discussion. We also thank T. Shibata, Y. Morishita, T. Kondo, and G. Sheng for critically reading the manuscript. This work was supported by a Grant-in-Aid for Scientific Research on Innovative Areas from MEXT Japan to S.H. and the RIKEN Foreign Postdoctoral Researcher Program to B.D.","year":"2014","publication":"Cell Reports","_id":"925","article_processing_charge":"No","page":"941 - 950","author":[{"full_name":"Dong, Bo","last_name":"Dong","first_name":"Bo"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","first_name":"Edouard B","last_name":"Hannezo"},{"first_name":"Shigeo","last_name":"Hayashi","full_name":"Hayashi, Shigeo"}],"date_updated":"2021-01-12T08:21:57Z","day":"22","abstract":[{"text":"The morphological stability of biological tubes is crucial for the efficient circulation of fluids and gases. Failure of this stability causes irregularly shaped tubes found in multiple pathological conditions. Here, we report that Drosophila mutants of the ESCRT III component Shrub/Vps32 exhibit a strikingly elongated sinusoidal tube phenotype. This is caused by excessive apical membrane synthesis accompanied by the ectopic accumulation and overactivation of Crumbs in swollen endosomes. Furthermore, we demonstrate that the apical extracellular matrix (aECM) of the tracheal tube is a viscoelastic material coupled with the apical membrane. We present a simple mechanical model in which aECM elasticity, apical membrane growth, and their interaction are three vital parameters determining the stability of biological tubes. Our findings demonstrate a mechanical role for the extracellular matrix and suggest that the interaction of the apical membrane and an elastic aECM determines the final morphology of biological tubes independent of cell shape.","lang":"eng"}],"type":"journal_article","oa_version":"None","month":"05","title":"Balance between apical membrane growth and luminal matrix resistance determines epithelial tubule shape","volume":7,"publist_id":"6515","date_created":"2018-12-11T11:49:14Z","status":"public","extern":"1","intvolume":"         7","language":[{"iso":"eng"}],"citation":{"ama":"Dong B, Hannezo EB, Hayashi S. Balance between apical membrane growth and luminal matrix resistance determines epithelial tubule shape. <i>Cell Reports</i>. 2014;7(4):941-950. doi:<a href=\"https://doi.org/10.1016/j.celrep.2014.03.066\">10.1016/j.celrep.2014.03.066</a>","mla":"Dong, Bo, et al. “Balance between Apical Membrane Growth and Luminal Matrix Resistance Determines Epithelial Tubule Shape.” <i>Cell Reports</i>, vol. 7, no. 4, Cell Press, 2014, pp. 941–50, doi:<a href=\"https://doi.org/10.1016/j.celrep.2014.03.066\">10.1016/j.celrep.2014.03.066</a>.","ista":"Dong B, Hannezo EB, Hayashi S. 2014. Balance between apical membrane growth and luminal matrix resistance determines epithelial tubule shape. Cell Reports. 7(4), 941–950.","apa":"Dong, B., Hannezo, E. B., &#38; Hayashi, S. (2014). Balance between apical membrane growth and luminal matrix resistance determines epithelial tubule shape. <i>Cell Reports</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.celrep.2014.03.066\">https://doi.org/10.1016/j.celrep.2014.03.066</a>","ieee":"B. Dong, E. B. Hannezo, and S. Hayashi, “Balance between apical membrane growth and luminal matrix resistance determines epithelial tubule shape,” <i>Cell Reports</i>, vol. 7, no. 4. Cell Press, pp. 941–950, 2014.","chicago":"Dong, Bo, Edouard B Hannezo, and Shigeo Hayashi. “Balance between Apical Membrane Growth and Luminal Matrix Resistance Determines Epithelial Tubule Shape.” <i>Cell Reports</i>. Cell Press, 2014. <a href=\"https://doi.org/10.1016/j.celrep.2014.03.066\">https://doi.org/10.1016/j.celrep.2014.03.066</a>.","short":"B. Dong, E.B. Hannezo, S. Hayashi, Cell Reports 7 (2014) 941–950."},"issue":"4","publication_status":"published","doi":"10.1016/j.celrep.2014.03.066","date_published":"2014-05-22T00:00:00Z"},{"status":"public","language":[{"iso":"eng"}],"citation":{"apa":"Hannezo, E. B., Prost, J., &#38; Joanny, J. (2014). Growth homeostatic regulation and stem cell dynamics in tissues. <i>Journal of the Royal Society Interface</i>. Royal Society of London. <a href=\"https://doi.org/10.1098/rsif.2013.0895\">https://doi.org/10.1098/rsif.2013.0895</a>","mla":"Hannezo, Edouard B., et al. “Growth Homeostatic Regulation and Stem Cell Dynamics in Tissues.” <i>Journal of the Royal Society Interface</i>, vol. 11, no. 93, Royal Society of London, 2014, doi:<a href=\"https://doi.org/10.1098/rsif.2013.0895\">10.1098/rsif.2013.0895</a>.","ista":"Hannezo EB, Prost J, Joanny J. 2014. Growth homeostatic regulation and stem cell dynamics in tissues. Journal of the Royal Society Interface. 11(93).","ama":"Hannezo EB, Prost J, Joanny J. Growth homeostatic regulation and stem cell dynamics in tissues. <i>Journal of the Royal Society Interface</i>. 2014;11(93). doi:<a href=\"https://doi.org/10.1098/rsif.2013.0895\">10.1098/rsif.2013.0895</a>","short":"E.B. Hannezo, J. Prost, J. Joanny, Journal of the Royal Society Interface 11 (2014).","chicago":"Hannezo, Edouard B, Jacques Prost, and Jean Joanny. “Growth Homeostatic Regulation and Stem Cell Dynamics in Tissues.” <i>Journal of the Royal Society Interface</i>. Royal Society of London, 2014. <a href=\"https://doi.org/10.1098/rsif.2013.0895\">https://doi.org/10.1098/rsif.2013.0895</a>.","ieee":"E. B. Hannezo, J. Prost, and J. Joanny, “Growth homeostatic regulation and stem cell dynamics in tissues,” <i>Journal of the Royal Society Interface</i>, vol. 11, no. 93. Royal Society of London, 2014."},"issue":"93","extern":"1","intvolume":"        11","publication_status":"published","doi":"10.1098/rsif.2013.0895","date_published":"2014-04-06T00:00:00Z","year":"2014","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Royal Society of London","acknowledgement":"We thank Jens Elgeti and Silvia Fre for fruitful discussions.","article_processing_charge":"No","publication":"Journal of the Royal Society Interface","_id":"926","day":"06","date_updated":"2021-01-12T08:21:57Z","abstract":[{"lang":"eng","text":"The regulation of cell growth in animal tissues is a question of critical importance: most tissues contain different types of cells in interconversion and the fraction of each type has to be controlled in a precise way, by mechanisms that remain unclear. Here, we provide a theoretical framework for the homeostasis of stem-cell-containing epithelial tissues using mechanical equations, which describe the size of the tissue and kinetic equations, which describe the interconversions of the cell populations. We show that several features, such as the evolution of stem cell fractions during intestinal development, the shape of a developing intestinal wall, as well as the increase in the proliferative compartment in cancer initiation, can be studied and understood from generic modelling which does not rely on a particular regulatory mechanism. Finally, inspired by recent experiments, we propose a model where cell division rates are regulated by the mechanical stresses in the epithelial sheet. We show that pressure-controlled growth can, in addition to the previous features, also explain with few parameters the formation of stem cell compartments as well as the morphologies observed when a colonic crypt becomes cancerous. We also discuss optimal strategies of wound healing, in connection with experiments on the cornea."}],"oa_version":"None","type":"journal_article","month":"04","author":[{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo"},{"first_name":"Jacques","last_name":"Prost","full_name":"Prost, Jacques"},{"last_name":"Joanny","first_name":"Jean","full_name":"Joanny, Jean"}],"date_created":"2018-12-11T11:49:14Z","publist_id":"6516","volume":11,"title":"Growth homeostatic regulation and stem cell dynamics in tissues"},{"citation":{"short":"E.B. Hannezo, J. Prost, J. Joanny, PNAS 111 (2014) 27–32.","ieee":"E. B. Hannezo, J. Prost, and J. Joanny, “Theory of epithelial sheet morphology in three dimensions,” <i>PNAS</i>, vol. 111, no. 1. National Academy of Sciences, pp. 27–32, 2014.","chicago":"Hannezo, Edouard B, Jacques Prost, and Jean Joanny. “Theory of Epithelial Sheet Morphology in Three Dimensions.” <i>PNAS</i>. National Academy of Sciences, 2014. <a href=\"https://doi.org/10.1073/pnas.1312076111\">https://doi.org/10.1073/pnas.1312076111</a>.","ista":"Hannezo EB, Prost J, Joanny J. 2014. Theory of epithelial sheet morphology in three dimensions. PNAS. 111(1), 27–32.","mla":"Hannezo, Edouard B., et al. “Theory of Epithelial Sheet Morphology in Three Dimensions.” <i>PNAS</i>, vol. 111, no. 1, National Academy of Sciences, 2014, pp. 27–32, doi:<a href=\"https://doi.org/10.1073/pnas.1312076111\">10.1073/pnas.1312076111</a>.","apa":"Hannezo, E. B., Prost, J., &#38; Joanny, J. (2014). Theory of epithelial sheet morphology in three dimensions. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1312076111\">https://doi.org/10.1073/pnas.1312076111</a>","ama":"Hannezo EB, Prost J, Joanny J. Theory of epithelial sheet morphology in three dimensions. <i>PNAS</i>. 2014;111(1):27-32. doi:<a href=\"https://doi.org/10.1073/pnas.1312076111\">10.1073/pnas.1312076111</a>"},"language":[{"iso":"eng"}],"issue":"1","extern":"1","intvolume":"       111","status":"public","doi":"10.1073/pnas.1312076111","date_published":"2014-01-01T00:00:00Z","publication_status":"published","article_processing_charge":"No","publication":"PNAS","_id":"927","year":"2014","publisher":"National Academy of Sciences","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"6517","date_created":"2018-12-11T11:49:14Z","title":"Theory of epithelial sheet morphology in three dimensions","volume":111,"date_updated":"2021-01-12T08:21:58Z","day":"01","abstract":[{"text":"Morphogenesis during embryo development requires the coordination of mechanical forces to generate the macroscopic shapes of organs. We propose a minimal theoretical model, based on cell adhesion and actomyosin contractility, which describes the various shapes of epithelial cells and the bending and buckling of epithelial sheets, as well as the relative stability of cellular tubes and spheres. We show that, to understand these processes, a full 3D description of the cells is needed, but that simple scaling laws can still be derived. The morphologies observed in vivo can be understood as stable points of mechanical equations and the transitions between them are either continuous or discontinuous. We then focus on epithelial sheet bending, a ubiquitous morphogenetic process. We calculate the curvature of an epithelium as a function of actin belt tension as well as of cell-cell and and cell-substrate tension. The model allows for a comparison of the relative stabilities of spherical or cylindrical cellular structures (acini or tubes). Finally, we propose a unique type of buckling instability of epithelia, driven by a flattening of individual cell shapes, and discuss experimental tests to verify our predictions.","lang":"eng"}],"oa_version":"None","type":"journal_article","month":"01","page":"27 - 32","author":[{"last_name":"Hannezo","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"full_name":"Prost, Jacques","first_name":"Jacques","last_name":"Prost"},{"first_name":"Jean","last_name":"Joanny","full_name":"Joanny, Jean"}]},{"main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2014.01.029","open_access":"1"}],"date_published":"2014-03-13T00:00:00Z","oa":1,"publication_status":"published","citation":{"chicago":"Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes.” <i>Cell</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">https://doi.org/10.1016/j.cell.2014.01.029</a>.","ieee":"J. T. Huff and D. Zilberman, “Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes,” <i>Cell</i>, vol. 156, no. 6. Elsevier, pp. 1286–1297, 2014.","short":"J.T. Huff, D. Zilberman, Cell 156 (2014) 1286–1297.","ama":"Huff JT, Zilberman D. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. <i>Cell</i>. 2014;156(6):1286-1297. doi:<a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">10.1016/j.cell.2014.01.029</a>","apa":"Huff, J. T., &#38; Zilberman, D. (2014). Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">https://doi.org/10.1016/j.cell.2014.01.029</a>","mla":"Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes.” <i>Cell</i>, vol. 156, no. 6, Elsevier, 2014, pp. 1286–97, doi:<a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">10.1016/j.cell.2014.01.029</a>.","ista":"Huff JT, Zilberman D. 2014. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell. 156(6), 1286–1297."},"extern":"1","intvolume":"       156","status":"public","external_id":{"pmid":["24630728"]},"date_created":"2021-06-04T12:00:16Z","volume":156,"date_updated":"2021-12-14T08:22:36Z","abstract":[{"text":"Dnmt1 epigenetically propagates symmetrical CG methylation in many eukaryotes. Their genomes are typically depleted of CG dinucleotides because of imperfect repair of deaminated methylcytosines. Here, we extensively survey diverse species lacking Dnmt1 and show that, surprisingly, symmetrical CG methylation is nonetheless frequently present and catalyzed by a different DNA methyltransferase family, Dnmt5. Numerous Dnmt5-containing organisms that diverged more than a billion years ago exhibit clustered methylation, specifically in nucleosome linkers. Clustered methylation occurs at unprecedented densities and directly disfavors nucleosomes, contributing to nucleosome positioning between clusters. Dense methylation is enabled by a regime of genomic sequence evolution that enriches CG dinucleotides and drives the highest CG frequencies known. Species with linker methylation have small, transcriptionally active nuclei that approach the physical limits of chromatin compaction. These features constitute a previously unappreciated genome architecture, in which dense methylation influences nucleosome positions, likely facilitating nuclear processes under extreme spatial constraints.","lang":"eng"}],"month":"03","type":"journal_article","oa_version":"Published Version","page":"1286-1297","_id":"9458","year":"2014","quality_controlled":"1","doi":"10.1016/j.cell.2014.01.029","publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"language":[{"iso":"eng"}],"issue":"6","title":"Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes","day":"13","author":[{"last_name":"Huff","first_name":"Jason T.","full_name":"Huff, Jason T."},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","last_name":"Zilberman","first_name":"Daniel"}],"article_processing_charge":"No","scopus_import":"1","article_type":"original","publication":"Cell","pmid":1,"department":[{"_id":"DaZi"}],"publisher":"Elsevier","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"National Academy of Sciences","pmid":1,"department":[{"_id":"DaZi"}],"publication":"Proceedings of the National Academy of Sciences","scopus_import":"1","article_processing_charge":"No","article_type":"original","author":[{"full_name":"Mérai, Zsuzsanna","first_name":"Zsuzsanna","last_name":"Mérai"},{"last_name":"Chumak","first_name":"Nina","full_name":"Chumak, Nina"},{"first_name":"Marcelina","last_name":"García-Aguilar","full_name":"García-Aguilar, Marcelina"},{"full_name":"Hsieh, Tzung-Fu","first_name":"Tzung-Fu","last_name":"Hsieh"},{"last_name":"Nishimura","first_name":"Toshiro","full_name":"Nishimura, Toshiro"},{"last_name":"Schoft","first_name":"Vera K.","full_name":"Schoft, Vera K."},{"first_name":"János","last_name":"Bindics","full_name":"Bindics, János"},{"last_name":"Ślusarz","first_name":"Lucyna","full_name":"Ślusarz, Lucyna"},{"last_name":"Arnoux","first_name":"Stéphanie","full_name":"Arnoux, Stéphanie"},{"last_name":"Opravil","first_name":"Susanne","full_name":"Opravil, Susanne"},{"first_name":"Karl","last_name":"Mechtler","full_name":"Mechtler, Karl"},{"last_name":"Zilberman","first_name":"Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel"},{"full_name":"Fischer, Robert L.","last_name":"Fischer","first_name":"Robert L."},{"full_name":"Tamaru, Hisashi","last_name":"Tamaru","first_name":"Hisashi"}],"day":"11","title":"The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes","language":[{"iso":"eng"}],"issue":"45","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"doi":"10.1073/pnas.1418564111","quality_controlled":"1","year":"2014","_id":"9479","page":"16166-16171","abstract":[{"lang":"eng","text":"Centromeres mediate chromosome segregation and are defined by the centromere-specific histone H3 variant (CenH3)/centromere protein A (CENP-A). Removal of CenH3 from centromeres is a general property of terminally differentiated cells, and the persistence of CenH3 increases the risk of diseases such as cancer. However, active mechanisms of centromere disassembly are unknown. Nondividing Arabidopsis pollen vegetative cells, which transport engulfed sperm by extended tip growth, undergo loss of CenH3; centromeric heterochromatin decondensation; and bulk activation of silent rRNA genes, accompanied by their translocation into the nucleolus. Here, we show that these processes are blocked by mutations in the evolutionarily conserved AAA-ATPase molecular chaperone, CDC48A, homologous to yeast Cdc48 and human p97 proteins, both of which are implicated in ubiquitin/small ubiquitin-like modifier (SUMO)-targeted protein degradation. We demonstrate that CDC48A physically associates with its heterodimeric cofactor UFD1-NPL4, known to bind ubiquitin and SUMO, as well as with SUMO1-modified CenH3 and mutations in NPL4 phenocopy cdc48a mutations. In WT vegetative cell nuclei, genetically unlinked ribosomal DNA (rDNA) loci are uniquely clustered together within the nucleolus and all major rRNA gene variants, including those rDNA variants silenced in leaves, are transcribed. In cdc48a mutant vegetative cell nuclei, however, these rDNA loci frequently colocalized with condensed centromeric heterochromatin at the external periphery of the nucleolus. Our results indicate that the CDC48ANPL4 complex actively removes sumoylated CenH3 from centromeres and disrupts centromeric heterochromatin to release bulk rRNA genes into the nucleolus for ribosome production, which fuels single nucleus-driven pollen tube growth and is essential for plant reproduction."}],"date_updated":"2021-12-14T08:23:26Z","oa_version":"Published Version","type":"journal_article","month":"11","volume":111,"date_created":"2021-06-07T07:23:43Z","status":"public","external_id":{"pmid":["25344531"]},"intvolume":"       111","extern":"1","citation":{"short":"Z. Mérai, N. Chumak, M. García-Aguilar, T.-F. Hsieh, T. Nishimura, V.K. Schoft, J. Bindics, L. Ślusarz, S. Arnoux, S. Opravil, K. Mechtler, D. Zilberman, R.L. Fischer, H. Tamaru, Proceedings of the National Academy of Sciences 111 (2014) 16166–16171.","chicago":"Mérai, Zsuzsanna, Nina Chumak, Marcelina García-Aguilar, Tzung-Fu Hsieh, Toshiro Nishimura, Vera K. Schoft, János Bindics, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA Genes.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2014. <a href=\"https://doi.org/10.1073/pnas.1418564111\">https://doi.org/10.1073/pnas.1418564111</a>.","ieee":"Z. Mérai <i>et al.</i>, “The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes,” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 45. National Academy of Sciences, pp. 16166–16171, 2014.","apa":"Mérai, Z., Chumak, N., García-Aguilar, M., Hsieh, T.-F., Nishimura, T., Schoft, V. K., … Tamaru, H. (2014). The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1418564111\">https://doi.org/10.1073/pnas.1418564111</a>","mla":"Mérai, Zsuzsanna, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA Genes.” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 45, National Academy of Sciences, 2014, pp. 16166–71, doi:<a href=\"https://doi.org/10.1073/pnas.1418564111\">10.1073/pnas.1418564111</a>.","ista":"Mérai Z, Chumak N, García-Aguilar M, Hsieh T-F, Nishimura T, Schoft VK, Bindics J, Ślusarz L, Arnoux S, Opravil S, Mechtler K, Zilberman D, Fischer RL, Tamaru H. 2014. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings of the National Academy of Sciences. 111(45), 16166–16171.","ama":"Mérai Z, Chumak N, García-Aguilar M, et al. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. <i>Proceedings of the National Academy of Sciences</i>. 2014;111(45):16166-16171. doi:<a href=\"https://doi.org/10.1073/pnas.1418564111\">10.1073/pnas.1418564111</a>"},"oa":1,"publication_status":"published","date_published":"2014-11-11T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1418564111","open_access":"1"}]},{"publication_identifier":{"eissn":["1878-4372"],"issn":["1360-1385"]},"doi":"10.1016/j.tplants.2014.01.014","quality_controlled":"1","issue":"5","language":[{"iso":"eng"}],"author":[{"last_name":"Kim","first_name":"M. Yvonne","full_name":"Kim, M. Yvonne"},{"first_name":"Daniel","last_name":"Zilberman","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"}],"day":"04","title":"DNA methylation as a system of plant genomic immunity","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"Elsevier","department":[{"_id":"DaZi"}],"pmid":1,"publication":"Trends in Plant Science","article_type":"review","article_processing_charge":"No","scopus_import":"1","publication_status":"published","date_published":"2014-05-04T00:00:00Z","status":"public","external_id":{"pmid":["24618094 "]},"intvolume":"        19","extern":"1","citation":{"ama":"Kim MY, Zilberman D. DNA methylation as a system of plant genomic immunity. <i>Trends in Plant Science</i>. 2014;19(5):320-326. doi:<a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">10.1016/j.tplants.2014.01.014</a>","apa":"Kim, M. Y., &#38; Zilberman, D. (2014). DNA methylation as a system of plant genomic immunity. <i>Trends in Plant Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">https://doi.org/10.1016/j.tplants.2014.01.014</a>","ista":"Kim MY, Zilberman D. 2014. DNA methylation as a system of plant genomic immunity. Trends in Plant Science. 19(5), 320–326.","mla":"Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant Genomic Immunity.” <i>Trends in Plant Science</i>, vol. 19, no. 5, Elsevier, 2014, pp. 320–26, doi:<a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">10.1016/j.tplants.2014.01.014</a>.","chicago":"Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant Genomic Immunity.” <i>Trends in Plant Science</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">https://doi.org/10.1016/j.tplants.2014.01.014</a>.","ieee":"M. Y. Kim and D. Zilberman, “DNA methylation as a system of plant genomic immunity,” <i>Trends in Plant Science</i>, vol. 19, no. 5. Elsevier, pp. 320–326, 2014.","short":"M.Y. Kim, D. Zilberman, Trends in Plant Science 19 (2014) 320–326."},"page":"320-326","type":"journal_article","month":"05","oa_version":"None","date_updated":"2021-12-14T08:24:48Z","abstract":[{"lang":"eng","text":"Transposons are selfish genetic sequences that can increase their copy number and inflict substantial damage on their hosts. To combat these genomic parasites, plants have evolved multiple pathways to identify and silence transposons by methylating their DNA. Plants have also evolved mechanisms to limit the collateral damage from the antitransposon machinery. In this review, we examine recent developments that have elucidated many of the molecular workings of these pathways. We also highlight the evidence that the methylation and demethylation pathways interact, indicating that plants have a highly sophisticated, integrated system of transposon defense that has an important role in the regulation of gene expression."}],"volume":19,"date_created":"2021-06-07T14:38:09Z","year":"2014","_id":"9519"},{"quality_controlled":"1","doi":"10.37236/3752","publication_identifier":{"eissn":["1077-8926"]},"language":[{"iso":"eng"}],"issue":"1","arxiv":1,"title":"On the number of spanning trees in random regular graphs","article_number":"P1.45","day":"28","author":[{"first_name":"Catherine","last_name":"Greenhill","full_name":"Greenhill, Catherine"},{"orcid":"0000-0002-4003-7567","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","full_name":"Kwan, Matthew Alan","first_name":"Matthew Alan","last_name":"Kwan"},{"full_name":"Wind, David","first_name":"David","last_name":"Wind"}],"scopus_import":"1","article_processing_charge":"No","article_type":"original","publication":"The Electronic Journal of Combinatorics","publisher":"The Electronic Journal of Combinatorics","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","main_file_link":[{"url":"https://doi.org/10.37236/3752","open_access":"1"}],"date_published":"2014-02-28T00:00:00Z","oa":1,"publication_status":"published","citation":{"apa":"Greenhill, C., Kwan, M. A., &#38; Wind, D. (2014). On the number of spanning trees in random regular graphs. <i>The Electronic Journal of Combinatorics</i>. The Electronic Journal of Combinatorics. <a href=\"https://doi.org/10.37236/3752\">https://doi.org/10.37236/3752</a>","ista":"Greenhill C, Kwan MA, Wind D. 2014. On the number of spanning trees in random regular graphs. The Electronic Journal of Combinatorics. 21(1), P1.45.","mla":"Greenhill, Catherine, et al. “On the Number of Spanning Trees in Random Regular Graphs.” <i>The Electronic Journal of Combinatorics</i>, vol. 21, no. 1, P1.45, The Electronic Journal of Combinatorics, 2014, doi:<a href=\"https://doi.org/10.37236/3752\">10.37236/3752</a>.","ama":"Greenhill C, Kwan MA, Wind D. On the number of spanning trees in random regular graphs. <i>The Electronic Journal of Combinatorics</i>. 2014;21(1). doi:<a href=\"https://doi.org/10.37236/3752\">10.37236/3752</a>","short":"C. Greenhill, M.A. Kwan, D. Wind, The Electronic Journal of Combinatorics 21 (2014).","chicago":"Greenhill, Catherine, Matthew Alan Kwan, and David Wind. “On the Number of Spanning Trees in Random Regular Graphs.” <i>The Electronic Journal of Combinatorics</i>. The Electronic Journal of Combinatorics, 2014. <a href=\"https://doi.org/10.37236/3752\">https://doi.org/10.37236/3752</a>.","ieee":"C. Greenhill, M. A. Kwan, and D. Wind, “On the number of spanning trees in random regular graphs,” <i>The Electronic Journal of Combinatorics</i>, vol. 21, no. 1. The Electronic Journal of Combinatorics, 2014."},"intvolume":"        21","extern":"1","status":"public","external_id":{"arxiv":["1309.6710"]},"date_created":"2021-06-23T06:29:35Z","volume":21,"abstract":[{"text":"Let d≥3 be a fixed integer. We give an asympotic formula for the expected number of spanning trees in a uniformly random d-regular graph with n vertices. (The asymptotics are as n→∞, restricted to even n if d is odd.) We also obtain the asymptotic distribution of the number of spanning trees in a uniformly random cubic graph, and conjecture that the corresponding result holds for arbitrary (fixed) d. Numerical evidence is presented which supports our conjecture.","lang":"eng"}],"date_updated":"2023-02-23T14:02:12Z","type":"journal_article","month":"02","oa_version":"Published Version","_id":"9594","year":"2014"},{"author":[{"first_name":"Andrew P","last_name":"Higginbotham","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P"},{"full_name":"Kuemmeth, Ferdinand","last_name":"Kuemmeth","first_name":"Ferdinand"},{"full_name":"Hanson, Micah","last_name":"Hanson","first_name":"Micah"},{"first_name":"Arthur","last_name":"Gossard","full_name":"Gossard, Arthur"},{"full_name":"Marcus, Charles","last_name":"Marcus","first_name":"Charles"}],"day":"14","article_number":"026801","arxiv":1,"title":"Coherent operations and screening in multielectron spin qubits","publist_id":"7958","publisher":"American Physiological Society","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication":"APS Physics, Physical Review Letters","doi":"10.1103/PhysRevLett.112.026801","quality_controlled":"1","issue":"2","language":[{"iso":"eng"}],"oa_version":"Preprint","type":"journal_article","month":"01","abstract":[{"text":"Multielectron spin qubits are demonstrated, and performance examined by comparing coherent exchange oscillations in coupled single-electron and multielectron quantum dots, measured in the same device. Fast (&gt;1 GHz) exchange oscillations with a quality factor Q∼15 are found for the multielectron case, compared to Q∼2 for the single-electron case, the latter consistent with experiments in the literature. A model of dephasing that includes voltage and hyperfine noise is developed that is in good agreement with both single- and multielectron data, though in both cases additional exchange-independent dephasing is needed to obtain quantitative agreement across a broad parameter range.","lang":"eng"}],"date_updated":"2021-01-12T08:22:14Z","volume":112,"date_created":"2018-12-11T11:44:36Z","acknowledgement":"The research is supported by the Intelligence Advanced Research Projects Activity (IARPA), through the Army Research Office Grant No. W911NF-12-1-0354, the DARPA QuEST Program, the Department of Energy, Office of Science, and the Danish National Research Foundation.","year":"2014","_id":"96","publication_status":"published","oa":1,"date_published":"2014-01-14T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1306.2720"}],"status":"public","external_id":{"arxiv":["1306.2720"]},"extern":"1","intvolume":"       112","citation":{"short":"A.P. Higginbotham, F. Kuemmeth, M. Hanson, A. Gossard, C. Marcus, APS Physics, Physical Review Letters 112 (2014).","chicago":"Higginbotham, Andrew P, Ferdinand Kuemmeth, Micah Hanson, Arthur Gossard, and Charles Marcus. “Coherent Operations and Screening in Multielectron Spin Qubits.” <i>APS Physics, Physical Review Letters</i>. American Physiological Society, 2014. <a href=\"https://doi.org/10.1103/PhysRevLett.112.026801\">https://doi.org/10.1103/PhysRevLett.112.026801</a>.","ieee":"A. P. Higginbotham, F. Kuemmeth, M. Hanson, A. Gossard, and C. Marcus, “Coherent operations and screening in multielectron spin qubits,” <i>APS Physics, Physical Review Letters</i>, vol. 112, no. 2. American Physiological Society, 2014.","apa":"Higginbotham, A. P., Kuemmeth, F., Hanson, M., Gossard, A., &#38; Marcus, C. (2014). Coherent operations and screening in multielectron spin qubits. <i>APS Physics, Physical Review Letters</i>. American Physiological Society. <a href=\"https://doi.org/10.1103/PhysRevLett.112.026801\">https://doi.org/10.1103/PhysRevLett.112.026801</a>","ista":"Higginbotham AP, Kuemmeth F, Hanson M, Gossard A, Marcus C. 2014. Coherent operations and screening in multielectron spin qubits. APS Physics, Physical Review Letters. 112(2), 026801.","mla":"Higginbotham, Andrew P., et al. “Coherent Operations and Screening in Multielectron Spin Qubits.” <i>APS Physics, Physical Review Letters</i>, vol. 112, no. 2, 026801, American Physiological Society, 2014, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.112.026801\">10.1103/PhysRevLett.112.026801</a>.","ama":"Higginbotham AP, Kuemmeth F, Hanson M, Gossard A, Marcus C. Coherent operations and screening in multielectron spin qubits. <i>APS Physics, Physical Review Letters</i>. 2014;112(2). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.112.026801\">10.1103/PhysRevLett.112.026801</a>"}},{"status":"public","external_id":{"pmid":["24698954"]},"citation":{"short":"M. Perkovic, M. Kunz, U. Endesfelder, S. Bunse, C. Wigge, Z. Yu, V.-V. Hodirnau, M.P. Scheffer, A. Seybert, S. Malkusch, E.M. Schuman, M. Heilemann, A.S. Frangakis, Journal of Structural Biology 186 (2014) 205–213.","ieee":"M. Perkovic <i>et al.</i>, “Correlative light- and electron microscopy with chemical tags,” <i>Journal of Structural Biology</i>, vol. 186, no. 2. Elsevier, pp. 205–213, 2014.","chicago":"Perkovic, Mario, Michael Kunz, Ulrike Endesfelder, Stefanie Bunse, Christoph Wigge, Zhou Yu, Victor-Valentin Hodirnau, et al. “Correlative Light- and Electron Microscopy with Chemical Tags.” <i>Journal of Structural Biology</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.jsb.2014.03.018\">https://doi.org/10.1016/j.jsb.2014.03.018</a>.","ista":"Perkovic M, Kunz M, Endesfelder U, Bunse S, Wigge C, Yu Z, Hodirnau V-V, Scheffer MP, Seybert A, Malkusch S, Schuman EM, Heilemann M, Frangakis AS. 2014. Correlative light- and electron microscopy with chemical tags. Journal of Structural Biology. 186(2), 205–213.","mla":"Perkovic, Mario, et al. “Correlative Light- and Electron Microscopy with Chemical Tags.” <i>Journal of Structural Biology</i>, vol. 186, no. 2, Elsevier, 2014, pp. 205–13, doi:<a href=\"https://doi.org/10.1016/j.jsb.2014.03.018\">10.1016/j.jsb.2014.03.018</a>.","apa":"Perkovic, M., Kunz, M., Endesfelder, U., Bunse, S., Wigge, C., Yu, Z., … Frangakis, A. S. (2014). Correlative light- and electron microscopy with chemical tags. <i>Journal of Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jsb.2014.03.018\">https://doi.org/10.1016/j.jsb.2014.03.018</a>","ama":"Perkovic M, Kunz M, Endesfelder U, et al. Correlative light- and electron microscopy with chemical tags. <i>Journal of Structural Biology</i>. 2014;186(2):205-213. doi:<a href=\"https://doi.org/10.1016/j.jsb.2014.03.018\">10.1016/j.jsb.2014.03.018</a>"},"intvolume":"       186","extern":"1","has_accepted_license":"1","publication_status":"published","oa":1,"date_published":"2014-05-01T00:00:00Z","ddc":["570"],"year":"2014","_id":"9655","month":"05","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Correlative microscopy incorporates the specificity of fluorescent protein labeling into high-resolution electron micrographs. Several approaches exist for correlative microscopy, most of which have used the green fluorescent protein (GFP) as the label for light microscopy. Here we use chemical tagging and synthetic fluorophores instead, in order to achieve protein-specific labeling, and to perform multicolor imaging. We show that synthetic fluorophores preserve their post-embedding fluorescence in the presence of uranyl acetate. Post-embedding fluorescence is of such quality that the specimen can be prepared with identical protocols for scanning electron microscopy (SEM) and transmission electron microscopy (TEM); this is particularly valuable when singular or otherwise difficult samples are examined. We show that synthetic fluorophores give bright, well-resolved signals in super-resolution light microscopy, enabling us to superimpose light microscopic images with a precision of up to 25 nm in the x–y plane on electron micrographs. To exemplify the preservation quality of our new method we visualize the molecular arrangement of cadherins in adherens junctions of mouse epithelial cells.","lang":"eng"}],"date_updated":"2021-07-22T08:26:32Z","page":"205-213","date_created":"2021-07-14T09:05:42Z","file_date_updated":"2021-07-22T08:06:34Z","volume":186,"issue":"2","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1047-8477"]},"quality_controlled":"1","doi":"10.1016/j.jsb.2014.03.018","pmid":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Elsevier","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0)","short":"CC BY-NC-ND (3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode","image":"/images/cc_by_nc_nd.png"},"article_type":"original","scopus_import":"1","article_processing_charge":"No","publication":"Journal of Structural Biology","file":[{"file_id":"9701","date_updated":"2021-07-22T08:06:34Z","checksum":"a322991b43cdc5935c99db88d285aa3a","date_created":"2021-07-22T08:06:34Z","access_level":"open_access","file_name":"2014_JournalOfStructuralBiology_Perkovic.pdf","success":1,"file_size":3454628,"content_type":"application/pdf","relation":"main_file","creator":"asandaue"}],"day":"01","author":[{"last_name":"Perkovic","first_name":"Mario","full_name":"Perkovic, Mario"},{"first_name":"Michael","last_name":"Kunz","full_name":"Kunz, Michael"},{"full_name":"Endesfelder, Ulrike","last_name":"Endesfelder","first_name":"Ulrike"},{"full_name":"Bunse, Stefanie","first_name":"Stefanie","last_name":"Bunse"},{"last_name":"Wigge","first_name":"Christoph","full_name":"Wigge, Christoph"},{"last_name":"Yu","first_name":"Zhou","full_name":"Yu, Zhou"},{"first_name":"Victor-Valentin","last_name":"Hodirnau","full_name":"Hodirnau, Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Margot P.","last_name":"Scheffer","full_name":"Scheffer, Margot P."},{"first_name":"Anja","last_name":"Seybert","full_name":"Seybert, Anja"},{"last_name":"Malkusch","first_name":"Sebastian","full_name":"Malkusch, Sebastian"},{"full_name":"Schuman, Erin M.","first_name":"Erin M.","last_name":"Schuman"},{"last_name":"Heilemann","first_name":"Mike","full_name":"Heilemann, Mike"},{"full_name":"Frangakis, Achilleas S.","first_name":"Achilleas S.","last_name":"Frangakis"}],"title":"Correlative light- and electron microscopy with chemical tags"},{"article_processing_charge":"No","scopus_import":"1","article_type":"original","publication":"The Journal of Chemical Physics","pmid":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"AIP Publishing","arxiv":1,"title":"Direct path integral estimators for isotope fractionation ratios","article_number":"244112","day":"28","author":[{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing","first_name":"Bingqing","last_name":"Cheng"},{"full_name":"Ceriotti, Michele","first_name":"Michele","last_name":"Ceriotti"}],"language":[{"iso":"eng"}],"issue":"24","quality_controlled":"1","doi":"10.1063/1.4904293","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"_id":"9662","year":"2014","date_created":"2021-07-15T09:22:49Z","volume":141,"abstract":[{"lang":"eng","text":"Fractionation of isotopes among distinct molecules or phases is a quantum effect which is often exploited to obtain insights on reaction mechanisms, biochemical, geochemical, and atmospheric phenomena. Accurate evaluation of isotope ratios in atomistic simulations is challenging, because one needs to perform a thermodynamic integration with respect to the isotope mass, along with time-consuming path integral calculations. By re-formulating the problem as a particle exchange in the ring polymer partition function, we derive new estimators giving direct access to the differential partitioning of isotopes, which can simplify the calculations by avoiding thermodynamic integration. We demonstrate the efficiency of these estimators by applying them to investigate the isotope fractionation ratios in the gas-phase Zundel cation, and in a few simple hydrocarbons."}],"date_updated":"2021-08-09T12:32:24Z","oa_version":"Preprint","type":"journal_article","month":"12","citation":{"ama":"Cheng B, Ceriotti M. Direct path integral estimators for isotope fractionation ratios. <i>The Journal of Chemical Physics</i>. 2014;141(24). doi:<a href=\"https://doi.org/10.1063/1.4904293\">10.1063/1.4904293</a>","mla":"Cheng, Bingqing, and Michele Ceriotti. “Direct Path Integral Estimators for Isotope Fractionation Ratios.” <i>The Journal of Chemical Physics</i>, vol. 141, no. 24, 244112, AIP Publishing, 2014, doi:<a href=\"https://doi.org/10.1063/1.4904293\">10.1063/1.4904293</a>.","ista":"Cheng B, Ceriotti M. 2014. Direct path integral estimators for isotope fractionation ratios. The Journal of Chemical Physics. 141(24), 244112.","apa":"Cheng, B., &#38; Ceriotti, M. (2014). Direct path integral estimators for isotope fractionation ratios. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.4904293\">https://doi.org/10.1063/1.4904293</a>","ieee":"B. Cheng and M. Ceriotti, “Direct path integral estimators for isotope fractionation ratios,” <i>The Journal of Chemical Physics</i>, vol. 141, no. 24. AIP Publishing, 2014.","chicago":"Cheng, Bingqing, and Michele Ceriotti. “Direct Path Integral Estimators for Isotope Fractionation Ratios.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2014. <a href=\"https://doi.org/10.1063/1.4904293\">https://doi.org/10.1063/1.4904293</a>.","short":"B. Cheng, M. Ceriotti, The Journal of Chemical Physics 141 (2014)."},"extern":"1","intvolume":"       141","status":"public","external_id":{"pmid":["25554138"],"arxiv":["1412.1308"]},"main_file_link":[{"url":"https://arxiv.org/abs/1412.1308","open_access":"1"}],"date_published":"2014-12-28T00:00:00Z","oa":1,"publication_status":"published"},{"_id":"9686","publication":"Philosophical Magazine","article_type":"original","scopus_import":"1","article_processing_charge":"No","publisher":"Taylor & Francis","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2014","volume":95,"title":"Strength of metals under vibrations – dislocation-density-function dynamics simulations","date_created":"2021-07-19T09:27:15Z","author":[{"orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing","last_name":"Cheng","first_name":"Bingqing"},{"full_name":"Leung, H.S.","first_name":"H.S.","last_name":"Leung"},{"last_name":"Ngan","first_name":"A.H.W.","full_name":"Ngan, A.H.W."}],"page":"1845-1865","type":"journal_article","oa_version":"None","month":"06","abstract":[{"text":"It is well known that ultrasonic vibration can soften metals, and this phenomenon has been widely exploited in industrial applications concerning metal forming and bonding. Recent experiments show that the simultaneous application of oscillatory stresses from audible to ultrasonic frequency ranges can lead to not only softening but also significant dislocation annihilation and subgrain formation in metal samples from the nano- to macro-size range. These findings indicate that the existing understanding of ultrasound softening – that the vibrations either impose additional stress waves to augment the quasi-static applied load, or cause heating of the metal, whereas the metal’s intrinsic deformation resistance or mechanism remains unaltered – is far from complete. To understand the softening and the associated enhanced subgrain formation and dislocation annihilation, a new simulator based on the dynamics of dislocation-density functions is employed. This new simulator considers the flux, production and annihilation, as well as the Taylor and elastic interactions between dislocation densities. Softening during vibrations as well as enhanced cell formation is predicted. The simulations reveal the main mechanism for subcell formation under oscillatory loadings to be the enhanced elimination of statistically stored dislocations (SSDs) by the oscillatory stress, leaving behind geometrically necessary dislocations with low Schmid factors which then form the subgrain walls. The oscillatory stress helps the depletion of the SSDs, because the chance for them to meet up and annihilate is increased with reversals of dislocation motions. This is the first simulation effort to successfully predict the cell formation phenomenon under vibratory loadings.","lang":"eng"}],"date_updated":"2023-02-23T14:04:59Z","day":"23","intvolume":"        95","extern":"1","issue":"16-18","language":[{"iso":"eng"}],"citation":{"ama":"Cheng B, Leung HS, Ngan AHW. Strength of metals under vibrations – dislocation-density-function dynamics simulations. <i>Philosophical Magazine</i>. 2014;95(16-18):1845-1865. doi:<a href=\"https://doi.org/10.1080/14786435.2014.897008\">10.1080/14786435.2014.897008</a>","apa":"Cheng, B., Leung, H. S., &#38; Ngan, A. H. W. (2014). Strength of metals under vibrations – dislocation-density-function dynamics simulations. <i>Philosophical Magazine</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/14786435.2014.897008\">https://doi.org/10.1080/14786435.2014.897008</a>","mla":"Cheng, Bingqing, et al. “Strength of Metals under Vibrations – Dislocation-Density-Function Dynamics Simulations.” <i>Philosophical Magazine</i>, vol. 95, no. 16–18, Taylor &#38; Francis, 2014, pp. 1845–65, doi:<a href=\"https://doi.org/10.1080/14786435.2014.897008\">10.1080/14786435.2014.897008</a>.","ista":"Cheng B, Leung HS, Ngan AHW. 2014. Strength of metals under vibrations – dislocation-density-function dynamics simulations. Philosophical Magazine. 95(16–18), 1845–1865.","chicago":"Cheng, Bingqing, H.S. Leung, and A.H.W. Ngan. “Strength of Metals under Vibrations – Dislocation-Density-Function Dynamics Simulations.” <i>Philosophical Magazine</i>. Taylor &#38; Francis, 2014. <a href=\"https://doi.org/10.1080/14786435.2014.897008\">https://doi.org/10.1080/14786435.2014.897008</a>.","ieee":"B. Cheng, H. S. Leung, and A. H. W. Ngan, “Strength of metals under vibrations – dislocation-density-function dynamics simulations,” <i>Philosophical Magazine</i>, vol. 95, no. 16–18. Taylor &#38; Francis, pp. 1845–1865, 2014.","short":"B. Cheng, H.S. Leung, A.H.W. Ngan, Philosophical Magazine 95 (2014) 1845–1865."},"status":"public","doi":"10.1080/14786435.2014.897008","date_published":"2014-06-23T00:00:00Z","quality_controlled":"1","publication_identifier":{"issn":["1478-6435"],"eissn":["1478-6443"]},"publication_status":"published"},{"year":"2014","acknowledgement":"We thank Michele Vendruscolo, Iskra Staneva, and William M. Jacobs, for helpful discussions. A.Š. acknowledges support from the Human Frontier Science Program and Emmanuel College. Y.C.C. and D.F. are supported by Engineering and Physical Sciences Research Council Programme Grant EP/I001352/1. T.P.J.K. acknowledges the Frances and Augustus Newman Foundation, the European Research Council, and the Biotechnology and Biological Sciences Research Council. D.F. acknowledges European Research Council Advanced Grant 227758.","_id":"10382","date_updated":"2021-11-29T13:29:05Z","abstract":[{"lang":"eng","text":"Protein oligomers have been implicated as toxic agents in a wide range of amyloid-related diseases. However, it has remained unsolved whether the oligomers are a necessary step in the formation of amyloid fibrils or just a dangerous byproduct. Analogously, it has not been resolved if the amyloid nucleation process is a classical one-step nucleation process or a two-step process involving prenucleation clusters. We use coarse-grained computer simulations to study the effect of nonspecific attractions between peptides on the primary nucleation process underlying amyloid fibrillization. We find that, for peptides that do not attract, the classical one-step nucleation mechanism is possible but only at nonphysiologically high peptide concentrations. At low peptide concentrations, which mimic the physiologically relevant regime, attractive interpeptide interactions are essential for fibril formation. Nucleation then inevitably takes place through a two-step mechanism involving prefibrillar oligomers. We show that oligomers not only help peptides meet each other but also, create an environment that facilitates the conversion of monomers into the β-sheet–rich form characteristic of fibrils. Nucleation typically does not proceed through the most prevalent oligomers but through an oligomer size that is only observed in rare fluctuations, which is why such aggregates might be hard to capture experimentally. Finally, we find that the nucleation of amyloid fibrils cannot be described by classical nucleation theory: in the two-step mechanism, the critical nucleus size increases with increases in both concentration and interpeptide interactions, which is in direct contrast with predictions from classical nucleation theory."}],"type":"journal_article","month":"12","oa_version":"Published Version","page":"17869-17874","date_created":"2021-11-29T13:09:53Z","volume":111,"external_id":{"pmid":["25453085"],"arxiv":["1412.0897"]},"status":"public","citation":{"short":"A. Šarić, Y.C. Chebaro, T.P.J. Knowles, D. Frenkel, Proceedings of the National Academy of Sciences 111 (2014) 17869–17874.","ieee":"A. Šarić, Y. C. Chebaro, T. P. J. Knowles, and D. Frenkel, “Crucial role of nonspecific interactions in amyloid nucleation,” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 50. National Academy of Sciences, pp. 17869–17874, 2014.","chicago":"Šarić, Anđela, Yassmine C. Chebaro, Tuomas P. J. Knowles, and Daan Frenkel. “Crucial Role of Nonspecific Interactions in Amyloid Nucleation.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2014. <a href=\"https://doi.org/10.1073/pnas.1410159111\">https://doi.org/10.1073/pnas.1410159111</a>.","ista":"Šarić A, Chebaro YC, Knowles TPJ, Frenkel D. 2014. Crucial role of nonspecific interactions in amyloid nucleation. Proceedings of the National Academy of Sciences. 111(50), 17869–17874.","mla":"Šarić, Anđela, et al. “Crucial Role of Nonspecific Interactions in Amyloid Nucleation.” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 50, National Academy of Sciences, 2014, pp. 17869–74, doi:<a href=\"https://doi.org/10.1073/pnas.1410159111\">10.1073/pnas.1410159111</a>.","apa":"Šarić, A., Chebaro, Y. C., Knowles, T. P. J., &#38; Frenkel, D. (2014). Crucial role of nonspecific interactions in amyloid nucleation. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1410159111\">https://doi.org/10.1073/pnas.1410159111</a>","ama":"Šarić A, Chebaro YC, Knowles TPJ, Frenkel D. Crucial role of nonspecific interactions in amyloid nucleation. <i>Proceedings of the National Academy of Sciences</i>. 2014;111(50):17869-17874. doi:<a href=\"https://doi.org/10.1073/pnas.1410159111\">10.1073/pnas.1410159111</a>"},"extern":"1","intvolume":"       111","oa":1,"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://www.pnas.org/content/111/50/17869"}],"date_published":"2014-12-01T00:00:00Z","pmid":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"National Academy of Sciences","article_processing_charge":"No","scopus_import":"1","article_type":"original","publication":"Proceedings of the National Academy of Sciences","day":"01","author":[{"last_name":"Šarić","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"full_name":"Chebaro, Yassmine C.","first_name":"Yassmine C.","last_name":"Chebaro"},{"full_name":"Knowles, Tuomas P. J.","first_name":"Tuomas P. J.","last_name":"Knowles"},{"first_name":"Daan","last_name":"Frenkel","full_name":"Frenkel, Daan"}],"arxiv":1,"title":"Crucial role of nonspecific interactions in amyloid nucleation","language":[{"iso":"eng"}],"issue":"50","keyword":["multidisciplinary"],"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"quality_controlled":"1","doi":"10.1073/pnas.1410159111"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"American Physical Society","pmid":1,"publication":"Physical Review E","article_processing_charge":"No","scopus_import":"1","article_type":"original","author":[{"first_name":"S. A.","last_name":"Mallory","full_name":"Mallory, S. A."},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","first_name":"Anđela","last_name":"Šarić"},{"last_name":"Valeriani","first_name":"C.","full_name":"Valeriani, C."},{"full_name":"Cacciuto, A.","first_name":"A.","last_name":"Cacciuto"}],"day":"06","title":"Anomalous thermomechanical properties of a self-propelled colloidal fluid","arxiv":1,"article_number":"052303","language":[{"iso":"eng"}],"issue":"5","publication_identifier":{"eissn":["1550-2376"],"issn":["1539-3755"]},"doi":"10.1103/physreve.89.052303","quality_controlled":"1","year":"2014","_id":"10383","date_updated":"2021-11-29T13:29:01Z","abstract":[{"text":"We use numerical simulations to compute the equation of state of a suspension of spherical self-propelled nanoparticles in two and three dimensions. We study in detail the effect of excluded volume interactions and confinement as a function of the system's temperature, concentration, and strength of the propulsion. We find a striking nonmonotonic dependence of the pressure on the temperature and provide simple scaling arguments to predict and explain the occurrence of such anomalous behavior. We explicitly show how our results have important implications for the effective forces on passive components suspended in a bath of active particles.","lang":"eng"}],"oa_version":"Preprint","type":"journal_article","month":"05","volume":89,"date_created":"2021-11-29T13:10:33Z","status":"public","external_id":{"pmid":["25353796"],"arxiv":["1310.0826"]},"intvolume":"        89","extern":"1","citation":{"short":"S.A. Mallory, A. Šarić, C. Valeriani, A. Cacciuto, Physical Review E 89 (2014).","ieee":"S. A. Mallory, A. Šarić, C. Valeriani, and A. Cacciuto, “Anomalous thermomechanical properties of a self-propelled colloidal fluid,” <i>Physical Review E</i>, vol. 89, no. 5. American Physical Society, 2014.","chicago":"Mallory, S. A., Anđela Šarić, C. Valeriani, and A. Cacciuto. “Anomalous Thermomechanical Properties of a Self-Propelled Colloidal Fluid.” <i>Physical Review E</i>. American Physical Society, 2014. <a href=\"https://doi.org/10.1103/physreve.89.052303\">https://doi.org/10.1103/physreve.89.052303</a>.","ista":"Mallory SA, Šarić A, Valeriani C, Cacciuto A. 2014. Anomalous thermomechanical properties of a self-propelled colloidal fluid. Physical Review E. 89(5), 052303.","mla":"Mallory, S. A., et al. “Anomalous Thermomechanical Properties of a Self-Propelled Colloidal Fluid.” <i>Physical Review E</i>, vol. 89, no. 5, 052303, American Physical Society, 2014, doi:<a href=\"https://doi.org/10.1103/physreve.89.052303\">10.1103/physreve.89.052303</a>.","apa":"Mallory, S. A., Šarić, A., Valeriani, C., &#38; Cacciuto, A. (2014). Anomalous thermomechanical properties of a self-propelled colloidal fluid. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physreve.89.052303\">https://doi.org/10.1103/physreve.89.052303</a>","ama":"Mallory SA, Šarić A, Valeriani C, Cacciuto A. Anomalous thermomechanical properties of a self-propelled colloidal fluid. <i>Physical Review E</i>. 2014;89(5). doi:<a href=\"https://doi.org/10.1103/physreve.89.052303\">10.1103/physreve.89.052303</a>"},"oa":1,"publication_status":"published","date_published":"2014-05-06T00:00:00Z","main_file_link":[{"url":"https://arxiv.org/abs/1310.0826","open_access":"1"}]},{"article_processing_charge":"No","publication":"ChemPhysChem","_id":"1058","year":"2014","publisher":"Wiley-Blackwell","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"6332","date_created":"2018-12-11T11:49:55Z","title":"Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang","volume":15,"abstract":[{"text":"Diffraction-unlimited far-field super-resolution fluorescence (nanoscopy) methods typically rely on transiently transferring fluorophores between two states, whereby this transfer is usually laid out as a switch. However, depending on whether this is induced in a spatially controlled manner using a pattern of light (coordinate-targeted) or stochastically on a single-molecule basis, specific requirements on the fluorophores are imposed. Therefore, the fluorophores are usually utilized just for one class of methods only. In this study we demonstrate that the reversibly switchable fluorescent protein Dreiklang enables live-cell recordings in both spatially controlled and stochastic modes. We show that the Dreiklang chromophore entails three different light-induced switching mechanisms, namely a reversible photochemical one, off-switching by stimulated emission, and a reversible transfer to a long-lived dark state from the S1 state, all of which can be utilized to overcome the diffraction barrier. We also find that for the single-molecule- based stochastic GSDIM approach (ground-state depletion followed by individual molecule return), Dreiklang provides a larger number of on-off localization events as compared to its progenitor Citrine. Altogether, Dreiklang is a versatile probe for essentially all popular forms of live-cell fluorescence nanoscopy.","lang":"eng"}],"day":"17","date_updated":"2021-01-12T06:47:58Z","oa_version":"None","month":"03","type":"journal_article","page":"756 - 762","author":[{"first_name":"Nickels","last_name":"Jensen","full_name":"Jensen, Nickels"},{"first_name":"Johann G","last_name":"Danzl","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G"},{"last_name":"Willig","first_name":"Katrin","full_name":"Willig, Katrin"},{"first_name":"Flavie","last_name":"Lavoie Cardinal","full_name":"Lavoie Cardinal, Flavie"},{"full_name":"Brakemann, Tanja","first_name":"Tanja","last_name":"Brakemann"},{"full_name":"Hell, Stefan","first_name":"Stefan","last_name":"Hell"},{"full_name":"Jakobs, Stefan","first_name":"Stefan","last_name":"Jakobs"}],"citation":{"short":"N. Jensen, J.G. Danzl, K. Willig, F. Lavoie Cardinal, T. Brakemann, S. Hell, S. Jakobs, ChemPhysChem 15 (2014) 756–762.","chicago":"Jensen, Nickels, Johann G Danzl, Katrin Willig, Flavie Lavoie Cardinal, Tanja Brakemann, Stefan Hell, and Stefan Jakobs. “Coordinate-Targeted and Coordinate-Stochastic Super-Resolution Microscopy with the Reversibly Switchable Fluorescent Protein Dreiklang.” <i>ChemPhysChem</i>. Wiley-Blackwell, 2014. <a href=\"https://doi.org/10.1002/cphc.201301034\">https://doi.org/10.1002/cphc.201301034</a>.","ieee":"N. Jensen <i>et al.</i>, “Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang,” <i>ChemPhysChem</i>, vol. 15, no. 4. Wiley-Blackwell, pp. 756–762, 2014.","apa":"Jensen, N., Danzl, J. G., Willig, K., Lavoie Cardinal, F., Brakemann, T., Hell, S., &#38; Jakobs, S. (2014). Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang. <i>ChemPhysChem</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/cphc.201301034\">https://doi.org/10.1002/cphc.201301034</a>","ista":"Jensen N, Danzl JG, Willig K, Lavoie Cardinal F, Brakemann T, Hell S, Jakobs S. 2014. Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang. ChemPhysChem. 15(4), 756–762.","mla":"Jensen, Nickels, et al. “Coordinate-Targeted and Coordinate-Stochastic Super-Resolution Microscopy with the Reversibly Switchable Fluorescent Protein Dreiklang.” <i>ChemPhysChem</i>, vol. 15, no. 4, Wiley-Blackwell, 2014, pp. 756–62, doi:<a href=\"https://doi.org/10.1002/cphc.201301034\">10.1002/cphc.201301034</a>.","ama":"Jensen N, Danzl JG, Willig K, et al. Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang. <i>ChemPhysChem</i>. 2014;15(4):756-762. doi:<a href=\"https://doi.org/10.1002/cphc.201301034\">10.1002/cphc.201301034</a>"},"language":[{"iso":"eng"}],"issue":"4","intvolume":"        15","extern":"1","status":"public","date_published":"2014-03-17T00:00:00Z","doi":"10.1002/cphc.201301034","publication_status":"published"},{"year":"2014","publisher":"Wiley-Blackwell","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","acknowledgement":"The Spanish MINECO project FIS2011-26675, the PIUNA program (U. Navarra), and the Project 29942WL (Fonds de Solidarité Prioritaire France-Cuba) have partially supported this research. ","publication":"Geophysical Research Letters","_id":"118","day":"16","date_updated":"2021-01-12T06:48:53Z","abstract":[{"text":"While the penetration of objects into granular media is well-studied, there is little understanding of how objects settle in gravities, geff, different from that of Earth - a scenario potentially relevant to the geomorphology of planets and asteroids and also to their exploration using man-made devices. By conducting experiments in an accelerating frame, we explore geff ranging from 0.4 g to 1.2 g. Surprisingly, we find that the rest depth is independent of geff and also that the time required for the object to come to rest scales like geff-1/2. With discrete element modeling simulations, we reproduce the experimental results and extend the range of geff to objects as small as asteroids and as large as Jupiter. Our results shed light on the initial stage of sedimentation into dry granular media across a range of celestial bodies and also have implications for the design of man-made, extraterrestrial vehicles and structures. Key Points The settling depth in granular media is independent of gravity The settling time scales like g-1/2 Layering driven by granular sedimentation should be similar.","lang":"eng"}],"oa_version":"None","month":"05","type":"journal_article","page":"3032 - 3037","author":[{"full_name":"Altshuler, Ernesto","first_name":"Ernesto","last_name":"Altshuler"},{"first_name":"H","last_name":"Torres","full_name":"Torres, H"},{"last_name":"González_Pita","first_name":"A","full_name":"González_Pita, A"},{"last_name":"Sánchez","first_name":"Colina G","full_name":"Sánchez, Colina G"},{"first_name":"Carlos","last_name":"Pérez Penichet","full_name":"Pérez Penichet, Carlos"},{"last_name":"Waitukaitis","first_name":"Scott R","full_name":"Waitukaitis, Scott R","orcid":"0000-0002-2299-3176","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hidalgo","first_name":"Rauól","full_name":"Hidalgo, Rauól"}],"date_created":"2018-12-11T11:44:43Z","publist_id":"7936","title":"Settling into dry granular media in different gravities","volume":41,"status":"public","language":[{"iso":"eng"}],"citation":{"mla":"Altshuler, Ernesto, et al. “Settling into Dry Granular Media in Different Gravities.” <i>Geophysical Research Letters</i>, vol. 41, no. 9, Wiley-Blackwell, 2014, pp. 3032–37, doi:<a href=\"https://doi.org/10.1002/2014GL059229\">10.1002/2014GL059229</a>.","ista":"Altshuler E, Torres H, González_Pita A, Sánchez CG, Pérez Penichet C, Waitukaitis SR, Hidalgo R. 2014. Settling into dry granular media in different gravities. Geophysical Research Letters. 41(9), 3032–3037.","apa":"Altshuler, E., Torres, H., González_Pita, A., Sánchez, C. G., Pérez Penichet, C., Waitukaitis, S. R., &#38; Hidalgo, R. (2014). Settling into dry granular media in different gravities. <i>Geophysical Research Letters</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/2014GL059229\">https://doi.org/10.1002/2014GL059229</a>","ama":"Altshuler E, Torres H, González_Pita A, et al. Settling into dry granular media in different gravities. <i>Geophysical Research Letters</i>. 2014;41(9):3032-3037. doi:<a href=\"https://doi.org/10.1002/2014GL059229\">10.1002/2014GL059229</a>","short":"E. Altshuler, H. Torres, A. González_Pita, C.G. Sánchez, C. Pérez Penichet, S.R. Waitukaitis, R. Hidalgo, Geophysical Research Letters 41 (2014) 3032–3037.","ieee":"E. Altshuler <i>et al.</i>, “Settling into dry granular media in different gravities,” <i>Geophysical Research Letters</i>, vol. 41, no. 9. Wiley-Blackwell, pp. 3032–3037, 2014.","chicago":"Altshuler, Ernesto, H Torres, A González_Pita, Colina G Sánchez, Carlos Pérez Penichet, Scott R Waitukaitis, and Rauól Hidalgo. “Settling into Dry Granular Media in Different Gravities.” <i>Geophysical Research Letters</i>. Wiley-Blackwell, 2014. <a href=\"https://doi.org/10.1002/2014GL059229\">https://doi.org/10.1002/2014GL059229</a>."},"issue":"9","extern":"1","intvolume":"        41","publication_status":"published","quality_controlled":"1","date_published":"2014-05-16T00:00:00Z","doi":"10.1002/2014GL059229"},{"oa":1,"publication_status":"published","date_published":"2014-10-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1402.0054"}],"status":"public","external_id":{"arxiv":["1402.0054"]},"extern":"1","related_material":{"record":[{"relation":"later_version","id":"11768","status":"public"}]},"citation":{"short":"M.H. Henzinger, S. Krinninger, D. Nanongkai, in:, 55th Annual Symposium on Foundations of Computer Science, Institute of Electrical and Electronics Engineers, 2014, pp. 146–155.","ieee":"M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Decremental single-source shortest paths on undirected graphs in near-linear total update time,” in <i>55th Annual Symposium on Foundations of Computer Science</i>, Philadelphia, PA, United States, 2014, pp. 146–155.","chicago":"Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “Decremental Single-Source Shortest Paths on Undirected Graphs in near-Linear Total Update Time.” In <i>55th Annual Symposium on Foundations of Computer Science</i>, 146–55. Institute of Electrical and Electronics Engineers, 2014. <a href=\"https://doi.org/10.1109/focs.2014.24\">https://doi.org/10.1109/focs.2014.24</a>.","ista":"Henzinger MH, Krinninger S, Nanongkai D. 2014. Decremental single-source shortest paths on undirected graphs in near-linear total update time. 55th Annual Symposium on Foundations of Computer Science. FOCS: Annual Symposium on Foundations of Computer Science, 146–155.","mla":"Henzinger, Monika H., et al. “Decremental Single-Source Shortest Paths on Undirected Graphs in near-Linear Total Update Time.” <i>55th Annual Symposium on Foundations of Computer Science</i>, Institute of Electrical and Electronics Engineers, 2014, pp. 146–55, doi:<a href=\"https://doi.org/10.1109/focs.2014.24\">10.1109/focs.2014.24</a>.","apa":"Henzinger, M. H., Krinninger, S., &#38; Nanongkai, D. (2014). Decremental single-source shortest paths on undirected graphs in near-linear total update time. In <i>55th Annual Symposium on Foundations of Computer Science</i> (pp. 146–155). Philadelphia, PA, United States: Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/focs.2014.24\">https://doi.org/10.1109/focs.2014.24</a>","ama":"Henzinger MH, Krinninger S, Nanongkai D. Decremental single-source shortest paths on undirected graphs in near-linear total update time. In: <i>55th Annual Symposium on Foundations of Computer Science</i>. Institute of Electrical and Electronics Engineers; 2014:146-155. doi:<a href=\"https://doi.org/10.1109/focs.2014.24\">10.1109/focs.2014.24</a>"},"page":"146-155","abstract":[{"lang":"eng","text":"The decremental single-source shortest paths (SSSP) problem concerns maintaining the distances between a given source node s to every node in an n-node m-edge graph G undergoing edge deletions. While its static counterpart can be easily solved in near-linear time, this decremental problem is much more challenging even in the undirected unweighted case. In this case, the classic O(mn) total update time of Even and Shiloach (JACM 1981) has been the fastest known algorithm for three decades. With the loss of a (1 + ε)-approximation factor, the running time was recently improved to O(n 2+o(1) ) by Bernstein and Roditty (SODA 2011), and more recently to O(n 1.8+o(1) + m 1+o(1) ) by Henzinger, Krinninger, and Nanongkai (SODA 2014). In this paper, we finally bring the running time of this case down to near-linear: We give a (1 + ε)-approximation algorithm with O(m 1+o(1) ) total update time, thus obtaining near-linear time. Moreover, we obtain O(m 1+o(1) log W) time for the weighted case, where the edge weights are integers from 1 to W. The only prior work on weighted graphs in o(mn log W) time is the O(mn 0.986 log W)-time algorithm by Henzinger, Krinninger, and Nanongkai (STOC 2014) which works for the general weighted directed case. In contrast to the previous results which rely on maintaining a sparse emulator, our algorithm relies on maintaining a so-called sparse (d, ε)-hop set introduced by Cohen (JACM 2000) in the PRAM literature. A (d, ε)-hop set of a graph G = (V, E) is a set E' of weighted edges such that the distance between any pair of nodes in G can be (1 + ε)-approximated by their d-hop distance (given by a path containing at most d edges) on G'=(V, E∪E'). Our algorithm can maintain an (n o(1) , ε)-hop set of near-linear size in near-linear time under edge deletions. It is the first of its kind to the best of our knowledge. To maintain the distances on this hop set, we develop a monotone bounded-hop Even-Shiloach tree. It results from extending and combining the monotone Even-Shiloach tree of Henzinger, Krinninger, and Nanongkai (FOCS 2013) with the bounded-hop SSSP technique of Bernstein (STOC 2013). These two new tools might be of independent interest."}],"date_updated":"2023-02-21T16:27:34Z","type":"conference","month":"10","oa_version":"Preprint","date_created":"2022-08-16T08:14:33Z","year":"2014","_id":"11855","publication_identifier":{"issn":["0272-5428"],"eisbn":["978-1-4799-6517-5"]},"doi":"10.1109/focs.2014.24","quality_controlled":"1","conference":{"end_date":"2014-10-21","location":"Philadelphia, PA, United States","name":"FOCS: Annual Symposium on Foundations of Computer Science","start_date":"2014-10-18"},"language":[{"iso":"eng"}],"author":[{"last_name":"Henzinger","first_name":"Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H"},{"full_name":"Krinninger, Sebastian","last_name":"Krinninger","first_name":"Sebastian"},{"full_name":"Nanongkai, Danupon","first_name":"Danupon","last_name":"Nanongkai"}],"day":"01","arxiv":1,"title":"Decremental single-source shortest paths on undirected graphs in near-linear total update time","publisher":"Institute of Electrical and Electronics Engineers","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"55th Annual Symposium on Foundations of Computer Science","scopus_import":"1","article_processing_charge":"No"},{"_id":"11870","year":"2014","date_created":"2022-08-16T09:41:57Z","type":"conference","month":"05","oa_version":"Preprint","date_updated":"2023-02-17T11:18:52Z","abstract":[{"text":"We consider dynamic algorithms for maintaining Single-Source Reachability (SSR) and approximate Single-Source Shortest Paths (SSSP) on n-node m-edge directed graphs under edge deletions (decremental algorithms). The previous fastest algorithm for SSR and SSSP goes back three decades to Even and Shiloach (JACM 1981); it has O(1) query time and O(mn) total update time (i.e., linear amortized update time if all edges are deleted). This algorithm serves as a building block for several other dynamic algorithms. The question whether its total update time can be improved is a major, long standing, open problem.\r\n\r\nIn this paper, we answer this question affirmatively. We obtain a randomized algorithm which, in a simplified form, achieves an Õ(mn0.984) expected total update time for SSR and (1 + ε)-approximate SSSP, where Õ(·) hides poly log n. We also extend our algorithm to achieve roughly the same running time for Strongly Connected Components (SCC), improving the algorithm of Roditty and Zwick (FOCS 2002), and an algorithm that improves the Õ (mn log W)-time algorithm of Bernstein (STOC 2013) for approximating SSSP on weighted directed graphs, where the edge weights are integers from 1 to W. All our algorithms have constant query time in the worst case.","lang":"eng"}],"citation":{"short":"M.H. Henzinger, S. Krinninger, D. Nanongkai, in:, 46th Annual ACM Symposium on Theory of Computing, Association for Computing Machinery, 2014.","chicago":"Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “Sublinear-Time Decremental Algorithms for Single-Source Reachability and Shortest Paths on Directed Graphs.” In <i>46th Annual ACM Symposium on Theory of Computing</i>. Association for Computing Machinery, 2014. <a href=\"https://doi.org/10.1145/2591796.2591869\">https://doi.org/10.1145/2591796.2591869</a>.","ieee":"M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Sublinear-time decremental algorithms for single-source reachability and shortest paths on directed graphs,” in <i>46th Annual ACM Symposium on Theory of Computing</i>, New York, NY, United States, 2014.","apa":"Henzinger, M. H., Krinninger, S., &#38; Nanongkai, D. (2014). Sublinear-time decremental algorithms for single-source reachability and shortest paths on directed graphs. In <i>46th Annual ACM Symposium on Theory of Computing</i>. New York, NY, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/2591796.2591869\">https://doi.org/10.1145/2591796.2591869</a>","mla":"Henzinger, Monika H., et al. “Sublinear-Time Decremental Algorithms for Single-Source Reachability and Shortest Paths on Directed Graphs.” <i>46th Annual ACM Symposium on Theory of Computing</i>, 674–683, Association for Computing Machinery, 2014, doi:<a href=\"https://doi.org/10.1145/2591796.2591869\">10.1145/2591796.2591869</a>.","ista":"Henzinger MH, Krinninger S, Nanongkai D. 2014. Sublinear-time decremental algorithms for single-source reachability and shortest paths on directed graphs. 46th Annual ACM Symposium on Theory of Computing. STOC: Symposium on Theory of Computing, 674–683.","ama":"Henzinger MH, Krinninger S, Nanongkai D. Sublinear-time decremental algorithms for single-source reachability and shortest paths on directed graphs. In: <i>46th Annual ACM Symposium on Theory of Computing</i>. Association for Computing Machinery; 2014. doi:<a href=\"https://doi.org/10.1145/2591796.2591869\">10.1145/2591796.2591869</a>"},"extern":"1","status":"public","external_id":{"arxiv":["1504.07959"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1504.07959"}],"date_published":"2014-05-01T00:00:00Z","publication_status":"published","oa":1,"article_processing_charge":"No","scopus_import":"1","publication":"46th Annual ACM Symposium on Theory of Computing","publisher":"Association for Computing Machinery","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"674 - 683","title":"Sublinear-time decremental algorithms for single-source reachability and shortest paths on directed graphs","arxiv":1,"day":"01","author":[{"full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","first_name":"Monika H"},{"full_name":"Krinninger, Sebastian","first_name":"Sebastian","last_name":"Krinninger"},{"first_name":"Danupon","last_name":"Nanongkai","full_name":"Nanongkai, Danupon"}],"language":[{"iso":"eng"}],"conference":{"start_date":"2014-05-31","name":"STOC: Symposium on Theory of Computing","location":"New York, NY, United States","end_date":"2014-06-03"},"quality_controlled":"1","doi":"10.1145/2591796.2591869","publication_identifier":{"issn":["0737-8017"],"isbn":["978-145032710-7"]}}]